The purpose was to prepare a (3-glycidoxypropyl)-trimethoxysilane (GPTMS)-SiO2 nanofluid and analyze the effect of nanofluid injection on carbonate reservoirs. GPTMS-modified silica nanoparticles (SNPs) were investigated by Fourier transform infrared spectroscopy (FTIR) and elemental analysis. FTIR spectra of C-H stretching vibrations at 2950 cm−1, indicating silica surface modification with GPTMS, were observed when the GPTMS in the feed was greater than 0.7 mmol/g. Further, a stable nanofluid was obtained when the amount of grafted silane was close to 0.73 mmol/g, the theoretical maximum amount of grafted silanes. To evaluate the performance of surface-modified SNPs for enhanced oil recovery in carbonate reservoirs, wettability alteration tests comprising flotation test and contact angle measurements using powder and plug samples of carbonates, respectively, were performed with different SNP concentrations. Powder samples were successfully changed from oil-wet to water-wet, and the contact angle of the plug sample decreased by up to 62.8% as a result of the reaction of the nanofluid; however, it did not reduce interfacial tension (IFT) as effectively as IFT reducer additives. A coreflooding test was conducted to determine the effective parameters of the enhanced oil recovery with the GPTMS-nanofluid, such as SNP concentration, injection rate, and rock properties. The nanofluid injection increased oil recovery by approximately 20% compared to conventional waterflooding through incremental oil recovery, mainly attributed to wettability alteration. Therefore, we expect the nanofluid to dramatically increase the oil recovery in strongly oil-wet carbonate reservoirs under high-salinity conditions.